How do you keep parts from showing through the skin on a transparent character?
Materials in Blender can be set to be transparent, so that light can pass through any objects using the material. Transparency is controlled using an “alpha” channel, where each pixel has an additional value, range 0-1, in addition to its RGB color values.
Transparency
So if you want an object to be transparent you could change (this can also be animated / keyed) the material and or alpha level of those objects you want to be transparent or solid.
Here's a detail link with a tutorial along with an example / walk through showing you how to do this.
Alpha / Transparency instructions
Video Link explaining Alpha / Transparency